Local pattern searching algorithm

[RickBioinf]

Hi everyone,

Does anybody maybe know of a good DNA and/or protein pattern searching algorithm that you can on your local server? I've been looking up a couple of them on the web, but they are all webserver based and also not a variable database. Any help is really appreciated.
Thanks for reading.

RickBioinf

[GenoMax]

You should be able to use "fuzznuc or fuzzpro" from EMBOSS which you can download here: http://emboss.sourceforge.net/download/

[RickBioinf]

Thanks for the info GenoMax, but unfortunately the link on the website, to download the tool, does not work. Do you have an idea if I can download it in another way?

Cheers

[RickBioinf]

Oops, forget it. It is already installed on Bio-linux.

Thanks again!

[GenoMax]

You are all set then.

On a different note: The EMBOSS link on the open-bio site seems to be redirecting to a lab: http://www.rudloff.se/ which does not seem to have the EMBOSS source code.

[maubp]

On a different note: The EMBOSS link on the open-bio site seems to be redirecting to a lab: http://www.rudloff.se/ which does not seem to have the EMBOSS source code.

Which link? Could you report this - eg to the EMBOSS mailing list?

[GenoMax]

Which link? Could you report this - eg to the EMBOSS mailing list?

The EMBOSS link under "Main Projects" at http://www.open-bio.org/wiki/Projects is http://emboss.sourceforge.net/ {It was corrected by Peter}. Looks like EMBOSS project lost that domain name.

[maubp]

Link fixed for now - and I've contacted the EMBOSS guys about the domain name... thanks!

[GenoMax]

Link fixed for now - and I've contacted the EMBOSS guys about the domain name... thanks!

Peter: Sorry to revive an old thread but the EMBOSS download appears to be messed up on the EBI mirror. Can you check with your contacts again?

[maubp]

At first glance ftp://emboss.open-bio.org/pub/EMBOSS/ and ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/ look OK, but the EBI mirror seems to be lacking some of the folders like the important "old" folder which holds each EMBOSS release. Is that what you meant?

[GenoMax]

@Peter: You must be seeing a cached version of the ftp site. Clicking on emboss-latest.tar.gz produces a "550 failed to change directory" error.

[maubp]

I would expect that to be a link to the current release, and right now none of the past EMBOSS releases seem to show up on the EBI mirror. I will email the EMBOSS guys.